From bb7cbcc5346e0702ca06a2ad4818f26e0943220f Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Thu, 23 Apr 2026 16:47:43 +0200 Subject: [PATCH 1/5] update imports to include BFO:0000054 and remove RO:0000056 --- src/ontology/imports/bfo_terms.txt | 3 +- src/ontology/imports/merged_import.owl | 56 ++++++++++++++++++++++++-- src/ontology/imports/ro_terms.txt | 1 - 3 files changed, 55 insertions(+), 5 deletions(-) diff --git a/src/ontology/imports/bfo_terms.txt b/src/ontology/imports/bfo_terms.txt index 9d4690e..80e16ae 100644 --- a/src/ontology/imports/bfo_terms.txt +++ b/src/ontology/imports/bfo_terms.txt @@ -1,4 +1,5 @@ BFO:0000015 BFO:0000019 BFO:0000034 -BFO:0000040 \ No newline at end of file +BFO:0000040 +BFO:0000054 \ No newline at end of file diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index 2928d32..f24c6c1 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2026-04-22") + +Annotation(owl:versionInfo "2026-04-23") Declaration(Class()) Declaration(Class()) @@ -34,6 +34,8 @@ Declaration(Class()) Declaration(Class()) Declaration(Class()) Declaration(Class()) +Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) @@ -74,7 +76,9 @@ Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(ObjectProperty()) +Declaration(ObjectProperty()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) Declaration(NamedIndividual()) @@ -155,7 +159,7 @@ AnnotationAssertion( "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") -# Annotation Property: (database_cross_reference) +# Annotation Property: (has cross-reference) AnnotationAssertion( "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string") AnnotationAssertion( "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.") @@ -183,6 +187,26 @@ AnnotationAssertion(rdfs:label (realized in) + +AnnotationAssertion( "this disease is realized in this disease course"@en) +AnnotationAssertion( "this fragility is realized in this shattering"@en) +AnnotationAssertion( "this investigator role is realized in this investigation"@en) +AnnotationAssertion(rdfs:label "realized in"@en) +InverseObjectProperties( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + +# Object Property: (realizes) + +AnnotationAssertion( "this disease course realizes this disease"@en) +AnnotationAssertion( "this investigation realizes this investigator role"@en) +AnnotationAssertion( "this shattering realizes this fragility"@en) +AnnotationAssertion( "Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process"@en) +AnnotationAssertion(rdfs:label "realizes"@en) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (preceded by) AnnotationAssertion( "x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point."@en) @@ -484,11 +508,35 @@ SubObjectPropertyOf( "molecular interaction relation helper property") SubObjectPropertyOf( ) +# Object Property: (realized in response to stimulus) + +AnnotationAssertion( "A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.") +AnnotationAssertion(rdfs:label "realized in response to stimulus") +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + # Object Property: (causally upstream of or within, positive effect) AnnotationAssertion(rdfs:label "causally upstream of or within, positive effect") SubObjectPropertyOf( ) +# Object Property: (realized in response to) + +AnnotationAssertion( "A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.") +AnnotationAssertion( "An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)") +AnnotationAssertion( "Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.") +AnnotationAssertion( "r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.") +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion( ) +AnnotationAssertion(Annotation( ) "triggered by process") +AnnotationAssertion(rdfs:label "realized in response to"@en) +SubObjectPropertyOf( ) +ObjectPropertyDomain( ) +ObjectPropertyRange( ) + ############################ @@ -841,7 +889,9 @@ AnnotationAssertion( "out of scope") +SubObjectPropertyOf(ObjectPropertyChain( ) ) SubObjectPropertyOf(ObjectPropertyChain( ) ) +SubObjectPropertyOf(ObjectPropertyChain( ) ) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) DLSafeRule(Body(ClassAtom( Variable()) ObjectPropertyAtom( Variable() Variable()))Head(ObjectPropertyAtom( Variable() Variable()))) diff --git a/src/ontology/imports/ro_terms.txt b/src/ontology/imports/ro_terms.txt index 2e7a3bb..f3ad407 100644 --- a/src/ontology/imports/ro_terms.txt +++ b/src/ontology/imports/ro_terms.txt @@ -1,4 +1,3 @@ RO:0000086 -RO:0000056 RO:0002233 RO:0002234 From 522649ec298c10e4296d719d1278fa089f3ee6e5 Mon Sep 17 00:00:00 2001 From: XimeAixa Date: Thu, 23 Apr 2026 09:58:44 -0500 Subject: [PATCH 2/5] new axiom for role in condensate assembly terms: realized in some biomolecular condensate formation --- src/ontology/idpo-edit.owl | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index aeaba3b..51c5116 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -737,6 +737,7 @@ AnnotationAssertion( "IDPO:0000061") AnnotationAssertion(rdfs:label "role in condensate assembly") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (driver role in condensate assembly) @@ -748,6 +749,7 @@ AnnotationAssertion( "IDPO:0000062") AnnotationAssertion(rdfs:label "driver role in condensate assembly") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (co-driver role in condensate assembly) @@ -758,6 +760,7 @@ AnnotationAssertion( "IDPO:0000063") AnnotationAssertion(rdfs:label "co-driver role in condensate assembly") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (regulator role in condensate assembly) @@ -768,6 +771,7 @@ AnnotationAssertion( "IDPO:0000064") AnnotationAssertion(rdfs:label "regulator role in condensate assembly") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (client role in condensate assembly) @@ -777,6 +781,7 @@ AnnotationAssertion( "IDPO:0000065") AnnotationAssertion(rdfs:label "client role in condensate assembly") SubClassOf( ) +SubClassOf( ObjectSomeValuesFrom( )) # Class: (protein aggregate formation) From 71a5fefa1dd448923e4a202d23ffae554a622855 Mon Sep 17 00:00:00 2001 From: XimeAixa Date: Thu, 23 Apr 2026 10:04:12 -0500 Subject: [PATCH 3/5] ontology roots fixed --- src/ontology/idpo-edit.owl | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 51c5116..901ff10 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -8,9 +8,11 @@ Prefix(rdfs:=) Ontology( Import() +Annotation( ) +Annotation( ) Annotation( ) -Annotation( ) -Annotation( ) +Annotation( ) +Annotation( ) Annotation( ) Annotation( "It describes structural aspects of an IDP/IDR, self-functions and functions directly associated with their disordered state.") Annotation( ) From 6103e06ad4e6d3d4afbb210cdf7aac4606b60988 Mon Sep 17 00:00:00 2001 From: XimeAixa Date: Tue, 28 Apr 2026 08:58:06 -0500 Subject: [PATCH 4/5] obo namespaces fixed --- src/ontology/idpo-edit.owl | 74 +++++++++++++++++++------------------- 1 file changed, 37 insertions(+), 37 deletions(-) diff --git a/src/ontology/idpo-edit.owl b/src/ontology/idpo-edit.owl index 901ff10..1535455 100644 --- a/src/ontology/idpo-edit.owl +++ b/src/ontology/idpo-edit.owl @@ -164,7 +164,7 @@ ObjectPropertyRange( "A quality of a protein region, defined by its conformational behavior.") AnnotationAssertion( "conformational state") AnnotationAssertion( "structural state") -AnnotationAssertion( "protein structural state") +AnnotationAssertion( "protein_structural_state") AnnotationAssertion( "IDPO:0000001") AnnotationAssertion(rdfs:label "protein structural state") SubClassOf( ) @@ -177,7 +177,7 @@ AnnotationAssertion(Annotation( "PMI AnnotationAssertion( "intrinsic disorder") AnnotationAssertion( "structural disorder") AnnotationAssertion( "unstructured") -AnnotationAssertion( "protein structural state") +AnnotationAssertion( "protein_structural_state") AnnotationAssertion( "flexible") AnnotationAssertion( "IDPO:0000002") AnnotationAssertion(rdfs:label "disorder state") @@ -187,7 +187,7 @@ SubClassOf( ) Annotation( "PMID:21961597") "Annotation DP01799r004") AnnotationAssertion(Annotation( "PMID:11910019") "A type of disorder state in which a protein region exhibits native-like secondary structure but lacks stable tertiary interactions.") -AnnotationAssertion( "protein structural state") +AnnotationAssertion( "protein_structural_state") AnnotationAssertion( "IDPO:0000003") AnnotationAssertion(rdfs:label "molten globule state") SubClassOf( ) @@ -196,7 +196,7 @@ SubClassOf( ) Annotation( "PMID:20817927") "Annotation DP04101r003") AnnotationAssertion(Annotation( "PMID:11910019") "A type of disorder state in which a protein region exhibits low compactness and residual or transiently populated secondary structure, representing an ensemble of rapidly interconverting conformations.") -AnnotationAssertion( "protein structural state") +AnnotationAssertion( "protein_structural_state") AnnotationAssertion( "IDPO:0000004") AnnotationAssertion(rdfs:label "pre-molten globule state") SubClassOf( ) @@ -206,7 +206,7 @@ SubClassOf( "A type of disorder state in which a protein region exhibits maximal conformational extension and minimal compaction, lacking stable secondary and tertiary structure.") AnnotationAssertion( "PMID:36368411") AnnotationAssertion( "native coil") -AnnotationAssertion( "protein structural state") +AnnotationAssertion( "protein_structural_state") AnnotationAssertion( "IDPO:0000005") AnnotationAssertion(rdfs:label "random coil state") SubClassOf( ) @@ -219,7 +219,7 @@ AnnotationAssertion( "structured state") AnnotationAssertion( "folded state") AnnotationAssertion( "globular conformation") -AnnotationAssertion( "protein structural state") +AnnotationAssertion( "protein_structural_state") AnnotationAssertion( "IDPO:0000006") AnnotationAssertion(rdfs:label "order state") SubClassOf( ) @@ -229,7 +229,7 @@ SubClassOf( "A protein structural state of a protein region for which a definitive structural state cannot be determined, due to insufficient or ambiguous evidence.") AnnotationAssertion( "structural state not defined") AnnotationAssertion( "undefined structural state") -AnnotationAssertion( "protein structural state") +AnnotationAssertion( "protein_structural_state") AnnotationAssertion( "inconclusive structural state") AnnotationAssertion( "indeterminate structural state") AnnotationAssertion( "IDPO:0000007") @@ -242,7 +242,7 @@ AnnotationAssertion( "PMID:38519511") AnnotationAssertion( "presumed order") AnnotationAssertion( "probably order") -AnnotationAssertion( "protein structural state") +AnnotationAssertion( "protein_structural_state") AnnotationAssertion( "IDPO:0000008") AnnotationAssertion(rdfs:label "likely order state") SubClassOf( ) @@ -252,7 +252,7 @@ SubClassOf( "A structurally undefined state of a protein region for which a definitive structural state cannot be determined, yet available data suggest it is disordered.") AnnotationAssertion( "presumed disorder") AnnotationAssertion( "probably disorder") -AnnotationAssertion( "protein structural state") +AnnotationAssertion( "protein_structural_state") AnnotationAssertion( "IDPO:0000009") AnnotationAssertion(rdfs:label "likely disorder state") SubClassOf( ) @@ -262,7 +262,7 @@ SubClassOf( "A dynamic process in which a protein region undergoes a reversible or irreversible transformation between defined structural states.") AnnotationAssertion( "conformational transition") AnnotationAssertion( "structural transition") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000010") AnnotationAssertion(rdfs:label "protein structural transition") SubClassOf( ) @@ -272,7 +272,7 @@ SubClassOf( ) Annotation( "PMID:38801244") "Annotation DP04243r004") AnnotationAssertion( "A structural transition in which a protein region changes from a disordered state to a fully ordered, well-defined three-dimensional conformation.") AnnotationAssertion( "structural ordering") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000011") AnnotationAssertion(rdfs:label "disorder to order") SubClassOf( ) @@ -283,7 +283,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:24356903") "Annotation DP01511r002") AnnotationAssertion( "A structural transition in which a protein changes from a molten globule state to a fully ordered, well-defined three-dimensional conformation.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000012") AnnotationAssertion(rdfs:label "molten globule to order") SubClassOf( ) @@ -294,7 +294,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:23462742") "Annotation DP02342r013") AnnotationAssertion( "A structural transition in which a protein region changes from a pre-molten globule to a fully ordered, well-defined three-dimensional conformation.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000013") AnnotationAssertion(rdfs:label "pre-molten globule to order") SubClassOf( ) @@ -306,7 +306,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:32817423") "Annotation DP03670r005") AnnotationAssertion( "A structural transition in which a protein region changes from an ordered state to a fully disordered conformation, losing secondary and tertiary structure elements.") AnnotationAssertion( "structural unfolding") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000014") AnnotationAssertion(rdfs:label "order to disorder") SubClassOf( ) @@ -316,7 +316,7 @@ SubClassOf( ObjectSomeValuesFrom( (order to molten globule) AnnotationAssertion( "A structural transition in which a protein region changes from an ordered state to a molten globule state, losing specific tertiary interactions while retaining native-like secondary structure.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000015") AnnotationAssertion(rdfs:label "order to molten globule") SubClassOf( ) @@ -326,7 +326,7 @@ SubClassOf( ObjectSomeValuesFrom( (order to pre-molten globule) AnnotationAssertion( "A structural transition in which a protein region changes from an ordered state to a pre-molten globule state, losing stable tertiary and secondary interactions and retaining only residual secondary structure elements.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000016") AnnotationAssertion(rdfs:label "order to pre-molten globule") SubClassOf( ) @@ -337,7 +337,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:29136196") "Annotation DP00207r012") AnnotationAssertion( "A structural transition in which a protein region changes from a disordered state to a molten globule state, by gaining native-like secondary structure elements.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000018") AnnotationAssertion(rdfs:label "disorder to molten globule") SubClassOf( ) @@ -348,7 +348,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:36037701") "Annotation DP03773r003") AnnotationAssertion( "A structural transition in which a protein region changes from a disordered state to a pre-molten globule state, by gaining residual or transiently populated secondary structure elements.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000019") AnnotationAssertion(rdfs:label "disorder to pre-molten globule") SubClassOf( ) @@ -358,7 +358,7 @@ SubClassOf( ObjectSomeValuesFrom( (molten globule to disorder) AnnotationAssertion( "A structural transition in which a protein region changes from a molten globule state to a fully disordered state, losing all secondary structure elements.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000020") AnnotationAssertion(rdfs:label "molten globule to disorder") SubClassOf( ) @@ -368,7 +368,7 @@ SubClassOf( ObjectSomeValuesFrom( (molten globule to pre-molten globule) AnnotationAssertion( "A structural transition in which a protein region changes from a molten globule state to a pre-molten globule state, losing native-like secondary structure, maintaining only residual secondary structure elements.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000021") AnnotationAssertion(rdfs:label "molten globule to pre-molten globule") SubClassOf( ) @@ -378,7 +378,7 @@ SubClassOf( ObjectSomeValuesFrom( (pre-molten globule to disorder) AnnotationAssertion( "A structural transition in which a protein region changes from a pre-molten globule state to a disordered state, losing residual or transiently populated secondary structure.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000022") AnnotationAssertion(rdfs:label "pre-molten globule to disorder") SubClassOf( ) @@ -389,7 +389,7 @@ SubClassOf( ObjectSomeValuesFrom( ) Annotation( "PMID:32338601") "Annotation DP00015r024") AnnotationAssertion( "A structural transition in which a protein region changes from a pre-molten glouble state to a molten globule state, by gaining native-like secondary structure elements.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000023") AnnotationAssertion(rdfs:label "pre-molten globule to molten globule") SubClassOf( ) @@ -403,7 +403,7 @@ AnnotationAssertion( "PMID:38287572") AnnotationAssertion(Annotation( ) "LLPS") AnnotationAssertion( "liquid–liquid demixing") -AnnotationAssertion( "higher-order assembly transition") +AnnotationAssertion( "higher-order_assembly_transition") AnnotationAssertion( "IDPO:0000025") AnnotationAssertion(rdfs:label "liquid-liquid phase separation") SubClassOf( ) @@ -417,7 +417,7 @@ AnnotationAssertion( "PMID:29358076") AnnotationAssertion( "condensate hardening") AnnotationAssertion( "condensate maturation") -AnnotationAssertion( "higher-order assembly transition") +AnnotationAssertion( "higher-order_assembly_transition") AnnotationAssertion( "IDPO:0000026") AnnotationAssertion(rdfs:label "condensate ageing") SubClassOf( ) @@ -430,7 +430,7 @@ AnnotationAssertion( "PMID:22579281") AnnotationAssertion( "liquid to gel transition") AnnotationAssertion( "condensate gelation") -AnnotationAssertion( "higher-order assembly transition") +AnnotationAssertion( "higher-order_assembly_transition") AnnotationAssertion( "IDPO:0000027") AnnotationAssertion(rdfs:label "gelation") SubClassOf( ) @@ -443,7 +443,7 @@ AnnotationAssertion(Annotation( "PMI AnnotationAssertion( ) AnnotationAssertion( "liquid to glass transition") AnnotationAssertion( "condensate crystallization") -AnnotationAssertion( "higher-order assembly transition") +AnnotationAssertion( "higher-order_assembly_transition") AnnotationAssertion( "IDPO:0000028") AnnotationAssertion(rdfs:label "crystallization") SubClassOf( ) @@ -793,7 +793,7 @@ AnnotationAssertion( "aggregate assembly") AnnotationAssertion( "aggregate formation") AnnotationAssertion( "protein aggregation") -AnnotationAssertion( "higher-order assembly transition") +AnnotationAssertion( "higher-order_assembly_transition") AnnotationAssertion( "IDPO:0000066") AnnotationAssertion(rdfs:label "protein aggregate formation") SubClassOf( ) @@ -803,7 +803,7 @@ SubClassOf( "PMID:40324497") "A protein aggregate formation leading to the formation of a protein aggregate lacking stable or ordered structure.") AnnotationAssertion( ) AnnotationAssertion( "PMID:26735904") -AnnotationAssertion( "higher-order assembly transition") +AnnotationAssertion( "higher-order_assembly_transition") AnnotationAssertion( "IDPO:0000067") AnnotationAssertion(rdfs:label "amorphous aggregate formation") SubClassOf( ) @@ -813,7 +813,7 @@ SubClassOf( "PMID:29602697") "A quality that describes the viscoelastic behavior and internal molecular organization of a condensate under given conditions, used to characterize proteins or protein regions that are part of the condensate.") AnnotationAssertion( "material state") AnnotationAssertion( "physical state") -AnnotationAssertion( "condensate material state") +AnnotationAssertion( "condensate_material_state") AnnotationAssertion( "IDPO:0000075") AnnotationAssertion(rdfs:label "condensate material state") SubClassOf( ) @@ -823,7 +823,7 @@ SubClassOf( ObjectSomeValuesFrom( "PMID:33510441") "A condensate state characterized by dynamic fusion, fission, dripping behavior, and rapid internal molecular rearrangements.") AnnotationAssertion( "PMID:38287572") -AnnotationAssertion( "condensate material state") +AnnotationAssertion( "condensate_material_state") AnnotationAssertion( "liquid-like condensate") AnnotationAssertion( "IDPO:0000076") AnnotationAssertion(rdfs:label "liquid-like condensate state") @@ -833,7 +833,7 @@ SubClassOf( "PMID:33510441") "A condensate state characterized by physical crosslinks between components, showing partial solid-like behavior while retaining some molecular mobility.") AnnotationAssertion( "PMID:34102212") -AnnotationAssertion( "condensate material state") +AnnotationAssertion( "condensate_material_state") AnnotationAssertion( "gel-like condensate") AnnotationAssertion( "IDPO:0000077") AnnotationAssertion(rdfs:label "gel-like condensate state") @@ -842,7 +842,7 @@ SubClassOf( (glass-like condensate state) AnnotationAssertion(Annotation( "PMID:33510441") "A condensate state characterized by gradually evolving mechanical properties, an absence of crystalline order, and no characteristic timescale for structural solidification.") -AnnotationAssertion( "condensate material state") +AnnotationAssertion( "condensate_material_state") AnnotationAssertion( "glass-like condensate") AnnotationAssertion( "IDPO:0000078") AnnotationAssertion(rdfs:label "glass-like condensate state") @@ -852,7 +852,7 @@ SubClassOf( "PMID:33510441") "A condensate state characterized by minimal internal molecular motion, typically arising through irreversible interactions or pathological ageing processes such as amyloid formation.") AnnotationAssertion( "PMID:34095780") -AnnotationAssertion( "condensate material state") +AnnotationAssertion( "condensate_material_state") AnnotationAssertion( "solid-like condensate") AnnotationAssertion( "IDPO:0000079") AnnotationAssertion(rdfs:label "solid-like condensate state") @@ -869,7 +869,7 @@ AnnotationAssertion(owl:deprecated # Class: (transition to a more ordered state) AnnotationAssertion( "A protein structural transition in which a protein or protein region gains secondary and/or tertiary structure, leading to a more compacted or ordered conformation.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000081") AnnotationAssertion(rdfs:label "transition to a more ordered state") SubClassOf( ) @@ -877,7 +877,7 @@ SubClassOf( (transition to a more disordered state) AnnotationAssertion( "A protein structural transition in which a protein or protein region loses secondary and/or tertiary structure, leading to a more extended or disordered conformation.") -AnnotationAssertion( "protein structural transition") +AnnotationAssertion( "protein_structural_transition") AnnotationAssertion( "IDPO:0000082") AnnotationAssertion(rdfs:label "transition to a more disordered state") SubClassOf( ) @@ -885,7 +885,7 @@ SubClassOf( (higher-order assembly transition) AnnotationAssertion(Annotation( "PMID:33510441") "A biophysical process in which a biomolecular condensate or aggregate is formed or undergoes a change in material state.") -AnnotationAssertion( "higher-order assembly transition") +AnnotationAssertion( "higher-order_assembly_transition") AnnotationAssertion( "IDPO:0000083") AnnotationAssertion(rdfs:label "higher-order assembly transition") SubClassOf( ) @@ -894,7 +894,7 @@ SubClassOf( "A higher-order assembly transition that concentrates specific biomolecules through weak, multivalent interactions. It may exhibit a well-mixed or spatially organized internal structure and can dynamically transition between different material states.") AnnotationAssertion( "biological condensate assembly") -AnnotationAssertion( "higher-order assembly transition") +AnnotationAssertion( "higher-order_assembly_transition") AnnotationAssertion( "membraneless organelle assembly") AnnotationAssertion( "non-membrane-bounded organelle assembly") AnnotationAssertion( "IDPO:0000084") From 6ed2c518801acddef73c9cc1bfe62a73cc138319 Mon Sep 17 00:00:00 2001 From: Ximeaixa Date: Tue, 5 May 2026 09:17:14 +0200 Subject: [PATCH 5/5] update imports --- src/ontology/imports/merged_import.owl | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/ontology/imports/merged_import.owl b/src/ontology/imports/merged_import.owl index f24c6c1..38dc0ee 100644 --- a/src/ontology/imports/merged_import.owl +++ b/src/ontology/imports/merged_import.owl @@ -7,8 +7,8 @@ Prefix(rdfs:=) Ontology( - -Annotation(owl:versionInfo "2026-04-23") + +Annotation(owl:versionInfo "2026-05-05") Declaration(Class()) Declaration(Class()) @@ -159,7 +159,7 @@ AnnotationAssertion( "has broad synonym"@en) AnnotationAssertion(rdfs:label "has_broad_synonym") -# Annotation Property: (has cross-reference) +# Annotation Property: (database_cross_reference) AnnotationAssertion( "disease characteristic (MONDO:0021125) has cross-reference (http://www.geneontology.org/formats/oboInOwl#hasDbXref) \"NCIT:C41009\"^^xsd:string") AnnotationAssertion( "An annotation property that links an ontology entity or a statement to a prefixed identifier or URI.")